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Add Casanovo-DB Functionality #325

Merged
merged 95 commits into from
Nov 18, 2024
Merged

Add Casanovo-DB Functionality #325

merged 95 commits into from
Nov 18, 2024

Commits on Mar 27, 2024

  1. begin adding tests for annotate mode

    @VarunAnanth2003
    VarunAnanth2003 committed Mar 27, 2024
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Commits on Mar 29, 2024

  1. add basic test for annotate mode

    @VarunAnanth2003
    VarunAnanth2003 committed Mar 29, 2024
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Commits on Apr 9, 2024

  1. added test case for annotate mode and modified method

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 9, 2024
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Commits on Apr 11, 2024

  1. very rough sketch of db upgrade (untested)

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 11, 2024
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Commits on Apr 15, 2024

  1. small upgrades to documentation

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 15, 2024
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  2. better output formatting

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 15, 2024
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Commits on Apr 27, 2024

  1. all tests added

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 27, 2024
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  2. remove minor debugging print statement

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 27, 2024
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  3. Generate new screengrabs with rich-codex

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    github-actions[bot] committed Apr 27, 2024
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  4. remove excess info logs, add monkeypatch to tests

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 27, 2024
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  5. Merge branch 'dev_db_search' of https://github.com/Noble-Lab/casanovo … 

    …into dev_db_search
    @VarunAnanth2003
    VarunAnanth2003 committed Apr 27, 2024
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  6. mp fix

    @VarunAnanth2003
    VarunAnanth2003 committed Apr 27, 2024
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Commits on May 7, 2024

  1. fix line lengths and modify test

    @VarunAnanth2003
    VarunAnanth2003 committed May 7, 2024
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  2. Generate new screengrabs with rich-codex

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  3. Merge branch 'dev' into dev_db_search 

    Move macOS test fixes from dev
    @VarunAnanth2003
    VarunAnanth2003 committed May 7, 2024
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  4. justins requested fixes

    @VarunAnanth2003
    VarunAnanth2003 committed May 7, 2024
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Commits on Jun 17, 2024

  1. added minor changes as requested by Wout

    @VarunAnanth2003
    VarunAnanth2003 committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. partial fixes requested by wout. Lots of subclassing removed

    @VarunAnanth2003
    VarunAnanth2003 committed Jun 18, 2024
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  2. documentation fixes and starting to cleanup batching code

    @VarunAnanth2003
    VarunAnanth2003 committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. cleaned up on_predict_batch_end, TODOs for calc_mz

    @VarunAnanth2003
    VarunAnanth2003 committed Jun 19, 2024
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Commits on Jun 27, 2024

  1. add proper calc_mz calculation with depthcharge

    @VarunAnanth2003
    VarunAnanth2003 committed Jun 27, 2024
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Commits on Jul 2, 2024

  1. rough implementation

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 2, 2024
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Commits on Jul 3, 2024

  1. tested implementation of db search

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 3, 2024
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  2. fix for issue with 0 candidates

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 3, 2024
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  3. minor fixes added

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 3, 2024
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  4. reordered and renamed variables for consistency

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 3, 2024
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Commits on Jul 4, 2024

  1. casanovo-db full working version with code simplification

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 4, 2024
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  2. Generate new screengrabs with rich-codex

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Commits on Jul 8, 2024

  1. fix batching issues

    @VarunAnanth2003
    VarunAnanth2003 committed Jul 8, 2024
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  2. Merge branch 'db_search_full' of https://github.com/Noble-Lab/casanovo … 

    …into db_search_full
    @VarunAnanth2003
    VarunAnanth2003 committed Jul 8, 2024
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Commits on Aug 12, 2024

  1. small fixes regarding documentation, import syntax, etc.

    @VarunAnanth2003
    VarunAnanth2003 committed Aug 12, 2024
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Commits on Aug 20, 2024

  1. add proteindatabase

    @VarunAnanth2003
    VarunAnanth2003 committed Aug 20, 2024
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  2. Generate new screengrabs with rich-codex

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Commits on Aug 21, 2024

  1. finish proteindatabase

    @VarunAnanth2003
    VarunAnanth2003 committed Aug 21, 2024
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  2. Merge branch 'db_search_full' of https://github.com/Noble-Lab/casanovo … 

    …into db_search_full
    @VarunAnanth2003
    VarunAnanth2003 committed Aug 21, 2024
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Commits on Aug 23, 2024

  1. all comments addressed

    @VarunAnanth2003
    VarunAnanth2003 committed Aug 23, 2024
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Commits on Aug 28, 2024

  1. new comments addressed

    @VarunAnanth2003
    VarunAnanth2003 committed Aug 28, 2024
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Commits on Sep 3, 2024

  1. final adjustments added

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 3, 2024
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  2. minor changes regarding formatting and small efficiency boosts

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 3, 2024
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  3. changes before reformatting config

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 3, 2024
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  4. replace all occurences of "max_length" with "max_peptide_len"

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 3, 2024
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  5. added nonspecific digestion

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 3, 2024
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Commits on Sep 13, 2024

  1. minor comments

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 13, 2024
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  2. full branch comments addressed

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 13, 2024
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  3. Merge pull request #352 from Noble-Lab/db_search_full 

    Full implementation of Casanovo-DB
    @VarunAnanth2003
    VarunAnanth2003 authored Sep 13, 2024
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  4. Merge branch 'dev' into dev_db_search

    @VarunAnanth2003
    VarunAnanth2003 authored Sep 13, 2024
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  5. Generate new screengrabs with rich-codex

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  6. updated and fixed failed tests

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 13, 2024
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Commits on Sep 14, 2024

  1. add mztab validation to dbsearch test

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 14, 2024
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Commits on Sep 17, 2024

  1. Merge branch 'dev' into dev_db_search

    @VarunAnanth2003
    VarunAnanth2003 authored Sep 17, 2024
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  2. lint fix

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 17, 2024
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  3. fix integration test

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 17, 2024
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  4. fix unit tests

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 17, 2024
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Commits on Sep 20, 2024

  1. Merge branch 'dev' into dev_db_search

    @VarunAnanth2003
    VarunAnanth2003 authored Sep 20, 2024
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Commits on Sep 21, 2024

  1. force fix test

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 21, 2024
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  2. clean up test_digest_fasta_enzyme

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 21, 2024
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  3. adjust test_digest_fasta_mods

    @VarunAnanth2003
    VarunAnanth2003 committed Sep 21, 2024
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Commits on Oct 2, 2024

  1. Merge branch 'dev' into dev_db_search

    @VarunAnanth2003
    VarunAnanth2003 committed Oct 2, 2024
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  2. allows top_match filtering for casanovo-db

    @VarunAnanth2003
    VarunAnanth2003 committed Oct 2, 2024
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  3. change default value for protein value in PepSpecMatch

    @VarunAnanth2003
    VarunAnanth2003 committed Oct 2, 2024
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  4. reverse issues with decoder

    @VarunAnanth2003
    VarunAnanth2003 committed Oct 2, 2024
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  5. update test and remove logging statement

    @VarunAnanth2003
    VarunAnanth2003 committed Oct 2, 2024
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Commits on Nov 3, 2024

  1. Merge branch 'dev' into dev_db_search

    @VarunAnanth2003
    VarunAnanth2003 authored Nov 3, 2024
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  2. db_utils fixes

    @VarunAnanth2003
    VarunAnanth2003 committed Nov 3, 2024
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  3. updates to dataloaders, model_runner, and model.py

    @VarunAnanth2003
    VarunAnanth2003 committed Nov 3, 2024
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  4. near final changes for all but db_utils

    @VarunAnanth2003
    VarunAnanth2003 committed Nov 3, 2024
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  5. line length fixes

    @VarunAnanth2003
    VarunAnanth2003 committed Nov 3, 2024
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Commits on Nov 10, 2024

  1. Minor refactoring and type hint fixes

    @bittremieux
    bittremieux committed Nov 10, 2024
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  2. Use mask for more efficient candidate filtering

    @bittremieux
    bittremieux committed Nov 10, 2024
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  3. Reorder methods in logical order

    @bittremieux
    bittremieux committed Nov 10, 2024
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  4. Fix unit tests

    @bittremieux
    bittremieux committed Nov 10, 2024
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  5. Directly generate DB peptides as DataFrame

    @bittremieux
    bittremieux committed Nov 10, 2024
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  6. Fix type hints and line lengths

    @bittremieux
    bittremieux committed Nov 10, 2024
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  7. Generate new screengrabs with rich-codex

    @github-actions
    github-actions[bot] committed Nov 10, 2024
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  8. Refactor batching to avoid code repetition

    @bittremieux
    bittremieux committed Nov 10, 2024
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  9. Merge remote-tracking branch 'origin/dev_db_search' into dev_db_search

    @bittremieux
    bittremieux committed Nov 10, 2024
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  10. More minor refactoring

    @bittremieux
    bittremieux committed Nov 10, 2024
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  11. Reformat with black

    @bittremieux
    bittremieux committed Nov 10, 2024
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  12. Minor fix

    @bittremieux
    bittremieux committed Nov 10, 2024
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  13. Fix output name crash

    @bittremieux
    bittremieux committed Nov 10, 2024
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  14. Fix AA score masking

    @bittremieux
    bittremieux committed Nov 10, 2024
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  15. Fix PSM export

    @bittremieux
    bittremieux committed Nov 10, 2024
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Commits on Nov 14, 2024

  1. Less verbose logging of skipped peptides

    @bittremieux
    bittremieux committed Nov 14, 2024
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  2. Appropriate end-of-run reporting

    @bittremieux
    bittremieux committed Nov 14, 2024
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  3. Fix PSM export from de novo

    @bittremieux
    bittremieux committed Nov 14, 2024
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  4. Generalize end-of-run reporting

    @bittremieux
    bittremieux committed Nov 14, 2024
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  5. Log additional information on spectra with no matching candidates

    @bittremieux
    bittremieux committed Nov 14, 2024
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  6. Fix linting issue

    @bittremieux
    bittremieux committed Nov 14, 2024
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  7. Fix some testing warnings

    @bittremieux
    bittremieux committed Nov 14, 2024
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  8. Log digestion settings

    @bittremieux
    bittremieux committed Nov 14, 2024
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  9. Reduce logging level for spectra without candidates

    @bittremieux
    bittremieux committed Nov 14, 2024
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Commits on Nov 18, 2024

  1. Round peptide masses for consistent sorting

    @bittremieux
    bittremieux committed Nov 18, 2024
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  2. Fox linting

    @bittremieux
    bittremieux committed Nov 18, 2024
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  3. Remove superfluous PSM export

    @bittremieux
    bittremieux committed Nov 18, 2024
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  4. Update changelog

    @bittremieux
    bittremieux committed Nov 18, 2024
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